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Related Concept Videos

Allosteric Proteins-ATCase01:19

Allosteric Proteins-ATCase

Binding sites linkages can regulate a protein's function.  For example, enzyme activity is often regulated through a feedback mechanism where the end product of the biochemical process serves as an inhibitor.
Aspartate transcarbamoylase (ATCase) is a cytosolic enzyme that catalyzes the condensation of L-aspartate and carbamoyl phosphate to  N-carbamoyl-L-aspartate. This reaction is the first step in pyrimidine biosynthesis. UTP and CTP, the end products of the pyrimidine synthesis pathway,...
Conserved Binding Sites01:49

Conserved Binding Sites

Many proteins’ biological role depends on their interactions with their ligands, small molecules that bind to specific locations on the protein known as ligand-binding sites. Ligand-binding sites are often conserved among homologous proteins as these sites are critical for protein function.
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally analyses the...
Ligand Binding and Linkage00:49

Ligand Binding and Linkage

Allosteric proteins have more than one ligand binding site; the binding of a ligand to any of these sites influences the binding of ligands to the other sites. When a protein is allosteric, its binding sites are called coupled or linked.  In the case of enzymes, the site that binds to the substrate is known as the active site and the other site is known as the regulatory site. When a ligand binds to the regulatory site, this leads to conformational changes in the protein that can influence the...

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Related Experiment Video

Updated: May 22, 2026

A Facile Protocol to Generate Site-Specifically Acetylated Proteins in Escherichia Coli
11:08

A Facile Protocol to Generate Site-Specifically Acetylated Proteins in Escherichia Coli

Published on: December 9, 2017

ASEB: a web server for KAT-specific acetylation site prediction.

Likun Wang1, Yipeng Du, Ming Lu

  • 1Institute of Systems Biomedicine, School of Basic Medical Sciences, Peking University Health Science Center, Beijing 100191, China.

Nucleic Acids Research
|May 19, 2012
PubMed
Summary

Predicting lysine acetyl-transferase (KAT) targets is crucial for understanding cell function. This study offers a web service for in silico prediction of KAT-specific acetylation sites, aiding experimental research.

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Site Specific Lysine Acetylation of Histones for Nucleosome Reconstitution using Genetic Code Expansion in Escherichia coli

Published on: December 26, 2020

Area of Science:

  • Biochemistry
  • Molecular Biology
  • Bioinformatics

Background:

  • Protein lysine acetylation is vital for cellular processes like gene regulation and metabolism.
  • Identifying the specific lysine (K)-acetyl-transferase (KAT) enzymes responsible for protein acetylation is experimentally challenging.
  • Accurate KAT substrate identification is essential for understanding acetylation's functional roles.

Purpose of the Study:

  • To provide a web service for in silico prediction of KAT-specific acetylation sites.
  • To offer an accessible online tool and R package based on the previously developed Acetylation Set Enrichment Based (ASEB) program.
  • To enhance prediction accuracy by integrating protein-protein interaction information.

Main Methods:

  • Development of a web server implementing the ASEB prediction method.
  • Inclusion of an R package for programmatic access to the prediction tool.
  • Integration of protein-protein interaction data to refine KAT-specific site predictions.

Main Results:

  • A functional web server for predicting KAT-specific acetylation sites is now available.
  • The web service provides both an online interface and an R package for the ASEB method.
  • Enhanced prediction accuracy through the incorporation of protein-protein interaction networks.

Conclusions:

  • The developed web server facilitates the identification of KAT-substrate relationships.
  • This resource aids researchers in directing experimental validation of acetylation sites.
  • The tool contributes to a deeper understanding of lysine acetylation in cellular regulation.